Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-002, A SH3 DOMAIN OF KIAA1010 PROTEIN [HOMO SAPIENS]
 
Authors :  T. Abe, H. Hirota, N. Kobayashi, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 Jun 03  (Deposition) - 28 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta Barrel, Sh3, Human Cdna, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Abe, H. Hirota, N. Kobayashi, F. Hayashi, S. Yokoyama
Solution Structure Of Rsgi Ruh-002, A Sh3 Domain Of Kiaa1010 Protein [Homo Sapiens]
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA1010 PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP021015-01
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    GeneKAZUSA CDNA HJ05262
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS SYSTEM

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UHC)

(-) Sites  (0, 0)

(no "Site" information available for 1UHC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UHC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UHC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UHC)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.DNMBP_HUMAN2-61
66-126
145-204
243-302
1513-1576
  1-
-
-
-
A:11-73

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003241091ENSE00001424407chr10:101769676-10176959582DNMBP_HUMAN-00--
1.2ENST000003241092ENSE00002142171chr10:101731891-101731737155DNMBP_HUMAN1-49490--
1.3ENST000003241093ENSE00001706506chr10:101728994-101728872123DNMBP_HUMAN49-90420--
1.4ENST000003241094ENSE00001719112chr10:101716962-1017149711992DNMBP_HUMAN90-7546650--
1.6ENST000003241096ENSE00001756411chr10:101668903-101668710194DNMBP_HUMAN754-818650--
1.7ENST000003241097ENSE00001121904chr10:101667851-101667752100DNMBP_HUMAN819-852340--
1.8ENST000003241098ENSE00001121895chr10:101659823-101659676148DNMBP_HUMAN852-901500--
1.10ENST0000032410910ENSE00001805771chr10:101658517-10165850018DNMBP_HUMAN901-90770--
1.12bENST0000032410912bENSE00002155272chr10:101658042-101657843200DNMBP_HUMAN907-974680--
1.13bENST0000032410913bENSE00001668127chr10:101656154-101656024131DNMBP_HUMAN974-1017440--
1.14ENST0000032410914ENSE00001784342chr10:101654807-101654703105DNMBP_HUMAN1018-1052350--
1.15bENST0000032410915bENSE00001699707chr10:101648710-101648582129DNMBP_HUMAN1053-1095430--
1.16bENST0000032410916bENSE00001760747chr10:101646389-101646057333DNMBP_HUMAN1096-12061110--
1.17ENST0000032410917ENSE00001671273chr10:101645623-101645444180DNMBP_HUMAN1207-1266600--
1.18ENST0000032410918ENSE00001705620chr10:101643966-101643768199DNMBP_HUMAN1267-1333670--
1.19ENST0000032410919ENSE00001624505chr10:101640118-101639568551DNMBP_HUMAN1333-15161841A:1-14 (gaps)36
1.20ENST0000032410920ENSE00001621278chr10:101637093-1016353341760DNMBP_HUMAN1517-1577611A:15-7561

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:79
 aligned with DNMBP_HUMAN | Q6XZF7 from UniProtKB/Swiss-Prot  Length:1577

    Alignment length:101
                                                                                                                         1577    
                                  1490      1500      1510      1520      1530      1540      1550      1560      1570      |  - 
         DNMBP_HUMAN   1481 GRNGQSQDLVKGCARTAQAPEDRSTEPDGSEAEGNQVYFAVYTFKARNPNELSVSANQKLKILEFKDVTGNTEWWLAEVNGKKGYVPSNYIRKTEYT----    -
               SCOP domains d1uhca                      _ A: Hypothetical protein Baa76854.1 (KIAA1010)                           SCOP domains
               CATH domains 1uhcA0                      0 A:1-79 SH3 Domains                                                      CATH domains
               Pfam domains --------------------------------------SH3_1-1uhcA01 A:17-66                             ------------- Pfam domains
         Sec.struct. author ......----------------------.........eee..................eeeeee.........eeeee....eeeee...eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------SH3  PDB: A:11-73 UniProt: 1513-1576                            ----- PROSITE
               Transcript 1 Exon 1.19  PDB: A:1-14 (gaps)       Exon 1.20  PDB: A:15-75 UniProt: 1517-1577                   ---- Transcript 1
                1uhc A    1 GSSGSS----------------------GSEAEGNQVYFAVYTFKARNPNELSVSANQKLKILEFKDVTGNTEWWLAEVNGKKGYVPSNYIRKTESGPSSG   79
                                 |   -         -        |8        18        28        38        48        58        68        78 
                                 6                      7                                                                        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: SH3 (175)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (DNMBP_HUMAN | Q6XZF7)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1uhc)
 
  Sites
(no "Sites" information available for 1uhc)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uhc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1uhc
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DNMBP_HUMAN | Q6XZF7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DNMBP_HUMAN | Q6XZF7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DNMBP_HUMAN | Q6XZF71ug1 4cc2 4cc3 4cc4 4cc7 4glm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UHC)